FMO DATABASE

FMODB ID: J3579

Calculation Name: 3UTM-C-Xray372

Preferred Name: Axin-1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3UTM

Chain ID: C

ChEMBL ID: CHEMBL4295996

UniProt ID: O35625

Base Structure: X-ray

Registration Date: 2023-06-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	32
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-76676.543695
FMO2-HF: Nuclear repulsion	64784.374143
FMO2-HF: Total energy	-11892.169552
FMO2-MP2: Total energy	-11927.070721

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(C:18:GLU)

Summations of interaction energy for fragment #1(C:18:GLU)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
2.644	-0.33899999999999	11.37	-3.61	-4.777	-0.001

Interaction energy analysis for fragmet #1(C:18:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.989 / q_NPA : -1.009

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

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Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	C	20	ALA	0	0.030	0.029	1.532	-7.594	-9.475	11.403	-5.028	-4.493	0.000
4	C	21	PRO	0	-0.031	-0.015	3.090	-0.645	-1.747	-0.033	1.418	-0.284	-0.001
5	C	22	ARG	1	0.971	0.976	5.419	-25.823	-25.823	0.000	0.000	0.000	0.000
6	C	23	PRO	0	-0.008	-0.005	5.642	-3.842	-3.842	0.000	0.000	0.000	0.000
7	C	24	PRO	0	0.002	0.000	8.912	-0.110	-0.110	0.000	0.000	0.000	0.000
8	C	25	VAL	0	-0.019	-0.015	12.277	0.865	0.865	0.000	0.000	0.000	0.000
9	C	26	PRO	0	-0.026	-0.015	13.142	-1.019	-1.019	0.000	0.000	0.000	0.000
10	C	27	GLY	0	-0.013	-0.009	16.377	-0.140	-0.140	0.000	0.000	0.000	0.000
11	C	28	GLU	-1	-0.954	-0.963	19.887	12.395	12.395	0.000	0.000	0.000	0.000
12	C	29	GLU	-1	-0.950	-0.971	22.506	13.127	13.127	0.000	0.000	0.000	0.000
13	C	30	GLY	0	-0.040	-0.017	24.929	-0.414	-0.414	0.000	0.000	0.000	0.000
14	C	60	THR	0	0.017	-0.006	31.990	-0.080	-0.080	0.000	0.000	0.000	0.000
15	C	61	PRO	0	0.007	-0.006	32.101	-0.126	-0.126	0.000	0.000	0.000	0.000
16	C	62	ARG	1	0.888	0.946	30.875	-8.267	-8.267	0.000	0.000	0.000	0.000
17	C	63	ARG	1	0.894	0.946	24.730	-10.762	-10.762	0.000	0.000	0.000	0.000
18	C	64	SER	0	0.008	0.009	26.376	-0.119	-0.119	0.000	0.000	0.000	0.000
19	C	65	ASP	-1	-0.922	-0.955	25.871	11.184	11.184	0.000	0.000	0.000	0.000
20	C	66	LEU	0	-0.019	-0.011	27.952	-0.237	-0.237	0.000	0.000	0.000	0.000
21	C	67	ASP	-1	-0.899	-0.949	30.591	8.202	8.202	0.000	0.000	0.000	0.000
22	C	68	LEU	0	-0.011	-0.016	29.844	-0.028	-0.028	0.000	0.000	0.000	0.000
23	C	69	GLY	0	-0.012	0.010	33.433	-0.081	-0.081	0.000	0.000	0.000	0.000
24	C	70	TYR	0	0.000	-0.005	34.578	0.233	0.233	0.000	0.000	0.000	0.000
25	C	71	GLU	-1	-0.921	-0.962	31.092	9.077	9.077	0.000	0.000	0.000	0.000
26	C	72	PRO	0	-0.054	-0.024	35.358	-0.196	-0.196	0.000	0.000	0.000	0.000
27	C	73	GLU	-1	-0.925	-0.952	37.511	7.160	7.160	0.000	0.000	0.000	0.000
28	C	74	GLY	0	-0.004	-0.010	38.827	-0.147	-0.147	0.000	0.000	0.000	0.000
29	C	75	SER	0	-0.042	-0.029	35.880	0.175	0.175	0.000	0.000	0.000	0.000
30	C	76	ALA	0	0.025	0.009	33.335	-0.150	-0.150	0.000	0.000	0.000	0.000
31	C	77	SER	0	-0.032	-0.019	34.936	-0.012	-0.012	0.000	0.000	0.000	0.000
32	C	78	PRO	0	0.000	0.025	36.894	0.018	0.018	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:18:GLU)